Assembly-Enabled Genome-Resolved Examinations of Microbiomes

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Using metagenome assembly we are actively characterizing the genomes of organisms in a wide variety of ecosystems, including oceans, rivers, lakes, soils, and numerous parts of the human microbiome. In many of these systems, we are establishing novel genome encyclopedias for organisms that have heretofore evaded cultivation or genomic characterizations. These datasets then enable more advanced analyses of metatranscriptomic and metaproteomic sequencing.

The approach has been developed into an institutional pipeline with multiple analysis options that can be tailored to the microbiome and question. This pipeline has been utilized for researchers from different JCVI departments and other institutions. We are leveraging this approach to examine gene-protein-function relationships in a variety of protein families. Additionally, we are beginning to develop a comprehensive understanding of the genome contents of various parts of the human microbiome, with the added understanding of how disease and the microbiome interact.